Interpretive Summary: A saturated genetic map of the tree crop, Theobroma cacao L. has long been desired to improve molecular breeding programs and ultimately germplasm resources. As part of the public-private cacao genome sequencing project, we have identified over 48,000 high quality Single Nucleotide Polymorphism (SNP) markers, and have selected 6,000 of these markers to genotype 1,152 individual cacao trees, including three distinct mapping populations. These genotypes were used to generate saturated genetic cacao maps, the preliminary results of this mapping is presented. Furthermore, the groundwork for the development of a standardized world-wide “core” set of SNP markers is established. This core set of markers will allow for the comparison of genotypes in breeding programs throughout the world thereby reducing mislabeled germplasm, and helping to ensure that the traits most desired by industry and farmers is represented in future distributed cultivars.

Technical Abstract:
Next Generation Sequencing technology is driving the sequencing and assembly of whole genomes at an ever increasing rate. With the release of the Theobroma cacao genome sequence, vast amounts of data are currently available to researchers worldwide, however mining this data to provide cacao breeders with the tools they need to produce improved plants remains an ongoing concern. To this end, we are using this data to develop new markers that will be immediately useful for cacao breeders. For example, as part of the genome sequencing project, a SNP discovery project was undertaken. Over 48,000 high quality SNPs were identified from 15 individual cacao lines, representing the 10 diverse STRUCTURE groups determined for cacao. These SNPs have been filtered for various purposes including the creation of a 6k Infinium genotyping SNP chip. This 6k chip is being used to genotype 1,152 individual cacao plants representing three different mapping populations. Data generated from this SNP chip will be mapped to help saturate existing cacao genetic maps. Furthermore, additional filtering has been performed to isolate different subsets of SNP markers. Combining all available SNP data to identify a "Core Set" of SNP markers to meet the genotyping needs of breeders is of critical importance to our future research goals. This Core Set will be utilized with a SNP assay optimized for use in cacao producer regions to allow for on-site genotyping.